Phonotactic patterns are commonly constrained by morphology. In English, for example, non-homorganic nasal–stop sequences are disallowed within morphemes but may occur across morpheme boundaries. This article demonstrates that similar effects of morphology on phonotactics can be found with non-concatenative morphology, even though they involve morphological domains that are more difficult to identify on the surface. Specifically, vowel alternation in a class of Egyptian Arabic verbs is affected by gradient phonotactic restrictions on consonant–vowel co-occurrence. However, such restrictions are only active in the imperfective form (e.g., [-rgaʕ] ‘return.ipfv’), not the perfective (e.g., [rigiʕ] ‘return.pfv’). Using a lexicon study and a wug test, I show that this pattern is in fact bounded by morphological domains and is reliably generalised by speakers when deriving novel forms. I compare accounts of this effect that differ on whether they require abstract morphosyntactic representations and non-concatenative morphemes and discuss their implications.